Coffee-planting in Wynaad declined and Alcock obtained a post a commission agent's office in Calcutta. This office closed soon and he worked from 1878-1880 in Purulia as an agent recruiting unskilled labourers for the Assam tea gardens. While here an acquaintance, Duncan Cameron, left him a Macmillan book by Michael FosterPhysiology Primer. This book, he wrote in his autobiographical notes, That little book was to me what the light from heaven was to St. Paul. It set my face towards natural science. He regretted that he never got to know Michael Foster, but throughout the rest of my life I have thought of him with the gratitude of a disciple, for his Primer and for his Textbook of Physiology which I got as soon as I had mastered his Primer. Its philosophical spirit impressed me very deeply.[1]

Another friend he made in Purulia was Lieut.-Col. J. J. Wood, then Deputy Sanitary Commissioner there. Wood invited him to the study of botany, natural history and chemistry. During this time Alcock even dug graves to study the bodies of humans. He studied bones using Holden's Osteology - Thence I crept on by means of a Nicholson's ' Manual of Zoology ' to the ' Descent of Man ' and the ' Origin of Species.' I was now resolved to be a doctor, but I could not think how it was to come to pass.[1]

Alcock sailed to India in 1886 and served in the north-west frontier with Sikh regiment and Punjab regiments. In Baluchistan he dealt with his first case of a fatal snake bite from an Echis carinatus. In 1888 he was offered the position of Surgeon-Naturalist to the Indian Marine Survey. He took it and joined the survey ship "Investigator" and remained until 1892. Here he studied marine zoology and he published many papers along with James Wood-Mason and others. He wrote about these years in A Naturalist in Indian Seas (1902) which is considered a classic in natural history travel.[1]

In 1892 Alcock resigned (having attained the rank of major)[2] and became Deputy Sanitary Commissioner for Eastern Bengal. In 1893 Wood-Mason went home and Alcock agreed to act for him during his absence. Wood-Mason died on his way to England and Alcock was appointed as the Superintendent of the Indian Museum. In 1895-96 he was on the Pamis Boundary Commission and wrote the Natural History results of this expedition. At the Indian Museum, Alcock worked on improving the public galleries of Reptiles, Fishes and Invertebrates. Sir George King who was the chairman of the Trustees supported him, however after his retirement, Alcock was given little support. Lord Curzon decided to exhibit the collections of the Indian Museum as a memorial to Queen Victoria in 1903 and Alcock was ordered to "vacate the gallery of Fishes at a moment's notice." Alcock protested to the Trustees that "it would be disgraceful to dismantle a gallery of Invertebrates which included an exhibit of the recent mosquito-malaria discoveries, at a moment when those discoveries seemed at last to have driven into the thickest British skull the great truth that the study of zoology was of some use to mankind." The gallery was spared but the library was to be cleared. These experiences caused Alcock to quit and he returned home in 1906 writing to the Government "telling him what an impossible post the Superintendentship of the Museum was and begging him to get it improved for the sake of the Science of Zoology and of my successors." In the letter Alcock wrote that Zoology was "a branch of pure science pregnant with human interest", important to the state "in matters of education, in matters agricultural and veterinary, and in the vital matter of public health." He suggested the establishment of "an Indian Zoological Survey" with a museum and laboratory administered by zoologists along the lines of the Geological and Botanical Surveys.[1]

He was asked to withdraw his resignation and rejoin with promises of reform at the Indian Museum, however he wrote that I stuck to my resolve that if the position at the Indian Museum was to be improved by my efforts no cynical potentate at Simla[3] should ever say that I had got it altered for my own benefit.[1]

Alcock was primarily a systematist, describing a wide range of species. He worked on aspects of biology and physiology of fishes, their distributions, evolution and behaviour. Some of his works were published in "Zoological Gleanings from the R.I.M.S. ' Investigator,' " published in " Scientific Memoirs by Medical Officers of the Army of India," Part XII, Simla, 1901.[1]

He worked on Fishes, Decapod Crustacea, and Deep Sea Madreporarian Corals. He published in the Journal of the Asiatic Society of Bengal, the Annals and Magazine of Natural History as well as catalogues published by the Indian Museum. His "Illustrations of the Zoology of the R.I.M.S. ' Investigator,' ", a series with illustrations by Indian artists (mainly A. C. Chowdhary and S. C. Mondul) has been considered as exceptional in beauty and accuracy.[1]

Alcock's school education of classics and literature led him to write in a Victorian literary style. Alcock also specialized in medical entomology and wrote a text book "Entomology for Medical Officers " (1st edition 1911, 2nd 1920). He also worked on a biography of Sir Patrick Manson.[1][4]

A guide to the zoological collections exhibited in the fish gallery of the Indian Museum (1899) (Scanned book)

Illustrations of the Zoology of the Royal Indian Marine Survey Ship Investigator, under the command of Commander T H Heming. Fishes Part V, Crustacea Part VI Mollusca Part II . Alfred Alcock. Calcutta, 1898 (scanned book)

A descriptive catalogue of the Indian deep-sea fishes in the Indian Museum : being a revised account of the deep-sea fishes collected by the Royal Indian marine survey ship Investigator (scanned book)